Matei David

SHRiMP2: Sensitive yet Practical Short Read Mapping

UNLABELLED We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures. AVAILABILITY SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.

Improved Separations between Nondeterministic and Randomized Multiparty Communication

We exhibit an explicit function <i>f</i> : {0, 1}ⁿ →{0, 1} that can be computed by a nondeterministic number-on-forehead protocol communicating <i>O</i>(log<i>n</i>) bits, but that requires <i>n</i>^Ω(1) bits of communication for randomized number-on-forehead protocols with <i>k</i> = <i>Δ</i>·log<i>n</i> players, for any fixed <i>Δ</i> < 1. Recent breakthrough results for the Set-Disjointness function [Lee and Shraibman 2008; Chattopadhyay and Ada 2008] based on the work of Sherstov [2009; 2008a] imply such a separation but only when the number of players is <i>k</i> < loglog<i>n</i>. We also show that for any <i>k</i> = <i>A</i> ·loglog<i>n</i> the above function <i>f</i> is computable by a small circuit whose depth is constant whenever <i>A</i> is a (possibly large) constant. Recent results again give such functions but only when the number of players is <i>k</i> < loglog<i>n</i>.

A Single-Enqueuer Wait-Free Queue Implementation

We study wait-free linearizable Queue implementations in asynchronous shared-memory systems from other consensus number 2 objects, such as Fetch&Add and Swap. The best previously known implementation allows at most two processes to perform Dequeue operations. We provide a new implementation, when only one process performs Enqueue operations and any number of processes perform Dequeue operations. A nice feature of this implementation is the fact that both Enqueue and Dequeue operations take constant time.

Detecting Alu insertions from high-throughput sequencing data

High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect, a tool that combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions directly in the vicinity of existing Alus. To set the parameters of our method, we use simulation of a faux reference, which allows us to compute the precision and recall of various parameter settings using real sequencing data. Applying our method to 100 bp paired Illumina data from seven individuals, including two trios, we detected on average 1519 novel Alus per sample. Based on the faux-reference simulation, we estimate that our method has 97% precision and 85% recall. We identify 808 novel Alus not previously described in other studies. We also demonstrate the use of alu-detect to study the local sequence and global location preferences for novel Alu insertions.

Separating Deterministic from Randomized Multiparty Communication Complexity

We solve some fundamental problems in the number-on-forehead (NOF) k- player communication model. We show that there exists a function which has at most logarithmic communication complexity for randomized protocols with one-sided false- positives error probability of 1/3, but which has linear communication complexity for deterministic protocols and, in fact, even for the more powerful nondeterministic protocols. The result holds for every e > 0 and every k 2 (1 e)n players, where n is the number of bits on each players forehead. As a consequence, we obtain the NOF communication class separation coRP6 NP. This in particular implies that P6 RP and NP6 coNP. We also show that for every e > 0 and every k n 1 e , there exists a function which has constant randomized complexity for public coin protocols but at least logarithmic complexity for private coin protocols. No larger gap between private and public coin protocols is possible. Our lower bounds are existential; no explicit function is known to satisfy nontrivial lower bounds for k log n players. However, for every e > 0 and every k (1 e) log n players, the NP6 coNP separation (and even the coNP6 MA separation) was obtained independently by Gavinsky and Sherstov (2010) using an explicit construction. In this work, for k (1=9) log n players, we exhibit an explicit function which has communication

Restricted stack implementations

We introduce a new object, BH, and prove that a system with one BH object and single-writer Registers has the same computational power as a system with countably many commutative and overwriting objects. This provides a simple characterization of the class of objects that can be implemented from commutative and overwriting objects, and creates a potential tool for proving impossibility results. It has been conjectured that Stacks and Queues shared by three or more processes are not in this class. In this paper, we use a BH object to show that two different restricted versions of Stacks are in this class. Specifically, we give an implementation of a Stack that supports any number of poppers, but at most two pushers. We also implement a Stack (or Queue) shared by any number of processes, but, in which, all stored elements are the same.

Assembly and characterization of novel Alu inserts detected from next-generation sequencing data

Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novel Alu inserts using their respective subfamily consensus sequences as references, we found an exponential decay in the Alu subfamily call enrichment with increased number of sequence variants (Pearson correlation , ). By mapping the sequences of these inserts to a human reference genome, we infer the reference Alu sources of a subset of the novel Alus, of which 85% were previously shown to be active. We also evaluate relationships between the loci of the novel inserts and their inferred sources.

Brief announcement: a single enqueuer wait-free queue implementation

The Queue is an important and well studied shared object type, used in many distributed algorithms. However, distributed systems usually provide lower-level types, such as Fetch&Add and Compare&Swap, so, in general, one has to implement a Queue object from the available base types. The Queue type supports Enqueue and Dequeue operations (a special value is returned when Dequeue is performed on an empty Queue), and it has consensus number 2. According to [2], wait-free Queue implementations exist in systems of n processes that provide objects with consensus number at least n. However, it is an open problem whether commonly available consensus number 2 types suffice to implement a wait-free Queue in a system with three or more processes. Afek, Weisberger and Weisman [1] consider the class Common2 of commutative and overwriting read-modify-write types, which includes most of the familiar consensus number 2 primitives such as Test&Set, Fetch&Add and Swap. They show that any consensus number 2 type can be used to implement any type in Common2 in a system with any number of processes. Hence, implementing a Queue from Common2 types is equivalent to implementing a Queue from an arbitrary consensus number 2 type. It is currently unknown if there exists a wait-free Queue implementation from Common2 types in a system with three or more processes. However, some restricted implementations exist. Herlihy and Wing [3] use Common2 types to implement a non-blocking Queue object shared by any number of processes, with the restriction that Dequeue operations are not defined when the Queue is empty. Using ideas from Herlihy’s universal construction in [2], Li modifies this implementation and obtains a wait-free Queue implementation from Common2 types for two dequeuers and any number ∗Supported by a Natural Sciences and Engineering Research Council of Canada PGS A scholarship.